Felipe Gomez Alonzo died because of influenza B being complicated by bacterial disease caused by sepsis, said the Foreign Ministry of Guatemala.
The minister's spokesperson Marta Larra said Guatemala officers had received an autopsy report on Monday.
Influenza B is a virus that causes seasonal diseases in most states of the United States, according to the Centers for Disease Control and Prevention.
The Medical Office of the New Mexico Office said it had not produced its autopsy report on Felipe's death, said Alexandra Sanchez, our office spokesperson.
The office said that Felipe had a test to Influenza B but there was no reason for death at the time.
CNN have taken out the decision of the US Customs and the protection of their territory for ideas.
The boy died on Christmas Eve at the Gerald Champion Regional Medical Center in Alamogordo, New Mexico, about 90 miles north of border crossing in El Paso, Texas.
He was kept out with his father for an illegal entry about 3 miles west of the porto del Pase port of El Paso.
Felipe was taken to hospital after a boundary agent saw symptoms of illness, and firstly medical staff admitted that they had a common cold and later discovered a fever.
"The child was held for an extra 90 minutes for watching and then released from the hospital on afternoon of 24 December with prescriptions for amoxicillin and Ibuprofen," said CBP in a report. T Amoxicillin is commonly used as an antibiotic.
The boy began to re-enter that night later and was taken to hospital for an assessment. He died again, said the CBP.
Felipe's body was brought back to Guatemala and he was sent to live in Yalambojoch in January, his half-sister said.
His father, Agustín Gómez Pérez, was released from CBP capt and is still in the United States, said a family member.
Felipe was the second child of Guatemala who died in the US patrol in December.
Jakelin Caal Maquin, 7, died in a two day hospital after taking her and her father to the Border Patrol station.
An autopsy report published last week revealed that she died from a threatening infection called streptococcal sepsis.
The disease was "fast-moving," caused the "metabolism of body and death," said the report from the medical examiner's office in El Paso County, Texas.
CNN presented Nicole Chavez to this report.